OpenRaiser/Intern-Atlas huggingface dataset:
Texture Synthesis with Spatial Generative Adversarial Networks
Venue: arXiv cs.CV 2017
Year: 2017

Generative adversarial networks (GANs) are a recent approach to train generative models of data, which have been shown to work particularly well on image data. In the current paper we introduce a new model for texture synthesis based on GAN learning. By extending the input noise distribution space from a single vector to a whole spatial tensor, we create an architecture with properties well suited to the task of texture synthesis, which we call spatial GAN (SGAN). To our knowledge, this is the first successful completely data-driven texture synthesis method based on GANs. Our method has the following features which make it a state of the art algorithm for texture synthesis: high image quality of the generated textures, very high scalability w.r.t. the output texture size, fast real-time forward generation, the ability to fuse multiple diverse source images in complex textures. To illustrate these capabilities we present multiple experiments with different classes of texture images and use cases. We also discuss some limitations of our method with respect to the types of texture images it can synthesize, and compare it to other neural techniques for texture generation.
Patient-Driven Privacy Control through Generalized Distillation
Venue: arXiv cs.CR 2017
Year: 2017

The introduction of data analytics into medicine has changed the nature of patient treatment. In this, patients are asked to disclose personal information such as genetic markers, lifestyle habits, and clinical history. This data is then used by statistical models to predict personalized treatments. However, due to privacy concerns, patients often desire to withhold sensitive information. This self-censorship can impede proper diagnosis and treatment, which may lead to serious health complications and even death over time. In this paper, we present privacy distillation, a mechanism which allows patients to control the type and amount of information they wish to disclose to the healthcare providers for use in statistical models. Meanwhile, it retains the accuracy of models that have access to all patient data under a sufficient but not full set of privacy-relevant information. We validate privacy distillation using a corpus of patients prescribed to warfarin for a personalized dosage. We use a deep neural network to implement privacy distillation for training and making dose predictions. We find that privacy distillation with sufficient privacy-relevant information i) retains accuracy almost as good as having all patient data (only 3\% worse), and ii) is effective at preventing errors that introduce health-related risks (only 3.9\% worse under- or over-prescriptions).
Convolutional Experts Constrained Local Model for Facial Landmark Detection
Venue: arXiv cs.CV 2017
Year: 2017

Constrained Local Models (CLMs) are a well-established family of methods for facial landmark detection. However, they have recently fallen out of favor to cascaded regression-based approaches. This is in part due to the inability of existing CLM local detectors to model the very complex individual landmark appearance that is affected by expression, illumination, facial hair, makeup, and accessories. In our work, we present a novel local detector -- Convolutional Experts Network (CEN) -- that brings together the advantages of neural architectures and mixtures of experts in an end-to-end framework. We further propose a Convolutional Experts Constrained Local Model (CE-CLM) algorithm that uses CEN as local detectors. We demonstrate that our proposed CE-CLM algorithm outperforms competitive state-of-the-art baselines for facial landmark detection by a large margin on four publicly-available datasets. Our approach is especially accurate and robust on challenging profile images.
Semi-supervised Learning using Denoising Autoencoders for Brain Lesion Detection and Segmentation
Venue: arXiv cs.CV 2017
Year: 2017

The work presented explores the use of denoising autoencoders (DAE) for brain lesion detection, segmentation and false positive reduction. Stacked denoising autoencoders (SDAE) were pre-trained using a large number of unlabeled patient volumes and fine tuned with patches drawn from a limited number of patients (n=20, 40, 65). The results show negligible loss in performance even when SDAE was fine tuned using 20 patients. Low grade glioma (LGG) segmentation was achieved using a transfer learning approach wherein a network pre-trained with High Grade Glioma (HGG) data was fine tuned using LGG image patches. The weakly supervised SDAE (for HGG) and transfer learning based LGG network were also shown to generalize well and provide good segmentation on unseen BraTS 2013 & BraTS 2015 test data. An unique contribution includes a single layer DAE, referred to as novelty detector(ND). ND was trained to accurately reconstruct non-lesion patches using a mean squared error loss function. The reconstruction error maps of test data were used to identify regions containing lesions. The error maps were shown to assign unique error distributions to various constituents of the glioma, enabling localization. The ND learns the non-lesion brain accurately as it was also shown to provide good segmentation performance on ischemic brain lesions in images from a different database.
Analyzing the group sparsity based on the rank minimization methods
Venue: arXiv cs.CV 2017
Year: 2017

Sparse coding has achieved a great success in various image processing studies. However, there is not any benchmark to measure the sparsity of image patch/group because sparse discriminant conditions cannot keep unchanged. This paper analyzes the sparsity of group based on the strategy of the rank minimization. Firstly, an adaptive dictionary for each group is designed. Then, we prove that group-based sparse coding is equivalent to the rank minimization problem, and thus the sparse coefficient of each group is measured by estimating the singular values of each group. Based on that measurement, the weighted Schatten $p$-norm minimization (WSNM) has been found to be the closest solution to the real singular values of each group. Thus, WSNM can be equivalently transformed into a non-convex $\ell_p$-norm minimization problem in group-based sparse coding. To make the proposed scheme tractable and robust, the alternating direction method of multipliers (ADMM) is used to solve the $\ell_p$-norm minimization problem. Experimental results on two applications: image inpainting and image compressive sensing (CS) recovery have shown that the proposed scheme outperforms many state-of-the-art methods.
Faster Randomized Worst-Case Update Time for Dynamic Subgraph Connectivity
Venue: arXiv cs.DS 2017
Year: 2017

Real-world networks are prone to breakdowns. Typically in the underlying graph $G$, besides the insertion or deletion of edges, the set of active vertices changes overtime. A vertex might work actively, or it might fail, and gets isolated temporarily. The active vertices are grouped as a set $S$. $S$ is subjected to updates, i.e., a failed vertex restarts, or an active vertex fails, and gets deleted from $S$. Dynamic subgraph connectivity answers the queries on connectivity between any two active vertices in the subgraph of $G$ induced by $S$. The problem is solved by a dynamic data structure, which supports the updates and answers the connectivity queries. In the general undirected graph, the best results for it include $\widetilde{O}(m^{2/3})$ deterministic amortized update time, $\widetilde{O}(m^{4/5})$ and $\widetilde{O}(\sqrt{mn})$ deterministic worst-case update time. In the paper, we propose a randomized data structure, which has $\widetilde{O}(m^{3/4})$ worst-case update time.
On Unique Decoding from Insertions and Deletions
Venue: arXiv cs.IT 2017
Year: 2017

In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used for long term data storage. We define natural probabilistic channels that make $t$ insertions or $t$ deletions, and study the probability of unique decoding. Our most substantial contribution is the derivation of tight upper bounds on the probability of unique decoding for messages passed though these channels. We also consider other aspects of the problem, and derive improved upper bounds for linear codes and VT-codes.
Times series averaging and denoising from a probabilistic perspective on time-elastic kernels
Venue: arXiv cs.LG 2017
Year: 2017

In the light of regularized dynamic time warping kernels, this paper re-considers the concept of time elastic centroid for a setof time series. We derive a new algorithm based on a probabilistic interpretation of kernel alignment matrices. This algorithm expressesthe averaging process in terms of a stochastic alignment automata. It uses an iterative agglomerative heuristic method for averagingthe aligned samples, while also averaging the times of occurrence of the aligned samples. By comparing classification accuracies for45 heterogeneous time series datasets obtained by first nearest centroid/medoid classifiers we show that: i) centroid-basedapproaches significantly outperform medoid-based approaches, ii) for the considered datasets, our algorithm that combines averagingin the sample space and along the time axes, emerges as the most significantly robust model for time-elastic averaging with apromising noise reduction capability. We also demonstrate its benefit in an isolated gesture recognition experiment and its ability tosignificantly reduce the size of training instance sets. Finally we highlight its denoising capability using demonstrative synthetic data:we show that it is possible to retrieve, from few noisy instances, a signal whose components are scattered in a wide spectral band.
The Emergence of Organizing Structure in Conceptual Representation
Venue: arXiv cs.LG 2017
Year: 2017

Both scientists and children make important structural discoveries, yet their computational underpinnings are not well understood. Structure discovery has previously been formalized as probabilistic inference about the right structural form --- where form could be a tree, ring, chain, grid, etc. [Kemp & Tenenbaum (2008). The discovery of structural form. PNAS, 105(3), 10687-10692]. While this approach can learn intuitive organizations, including a tree for animals and a ring for the color circle, it assumes a strong inductive bias that considers only these particular forms, and each form is explicitly provided as initial knowledge. Here we introduce a new computational model of how organizing structure can be discovered, utilizing a broad hypothesis space with a preference for sparse connectivity. Given that the inductive bias is more general, the model's initial knowledge shows little qualitative resemblance to some of the discoveries it supports. As a consequence, the model can also learn complex structures for domains that lack intuitive description, as well as predict human property induction judgments without explicit structural forms. By allowing form to emerge from sparsity, our approach clarifies how both the richness and flexibility of human conceptual organization can coexist.
Environmental Bisimulations for Delimited-Control Operators with Dynamic Prompt Generation
Venue: arXiv cs.PL 2017
Year: 2017

We present sound and complete environmental bisimilarities for a variant of Dybvig et al.'s calculus of multi-prompted delimited-control operators with dynamic prompt generation. The reasoning principles that we obtain generalize and advance the existing techniques for establishing program equivalence in calculi with single-prompted delimited control. The basic theory that we develop is presented using Madiot et al.'s framework that allows for smooth integration and composition of up-to techniques facilitating bisimulation proofs. We also generalize the framework in order to express environmental bisimulations that support equivalence proofs of evaluation contexts representing continuations. This change leads to a novel and powerful up-to technique enhancing bisimulation proofs in the presence of control operators.
Formal Languages, Formally and Coinductively
Venue: arXiv cs.LO 2017
Year: 2017

Traditionally, formal languages are defined as sets of words. More recently, the alternative coalgebraic or coinductive representation as infinite tries, i.e., prefix trees branching over the alphabet, has been used to obtain compact and elegant proofs of classic results in language theory. In this article, we study this representation in the Isabelle proof assistant. We define regular operations on infinite tries and prove the axioms of Kleene algebra for those operations. Thereby, we exercise corecursion and coinduction and confirm the coinductive view being profitable in formalizations, as it improves over the set-of-words view with respect to proof automation.
Batch and PIR Codes and Their Connections to Locally Repairable Codes
Venue: arXiv cs.IT 2017
Year: 2017

In this survey, two related families of codes are discussed: batch codes and codes for private information retrieval. These two families can be viewed as natural generalizations of locally repairable codes, which were extensively studied in the context of coding for fault tolerance in distributed data storage systems. Bounds on the parameters of the codes, as well as basic constructions, are presented. Connections between different code families are discussed.
Scalable Similarity Search for Molecular Descriptors
Venue: arXiv cs.DS 2017
Year: 2017

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solutions for more general integer vectors are in their infancy. In this paper we present a time- and space- efficient index for the problem that we call the succinct intervals-splitting tree algorithm for molecular descriptors (SITAd). Our approach extends efficient methods for binary-vector databases, and uses ideas from succinct data structures. Our experiments, on a large database of over 40 million compounds, show SITAd significantly outperforms alternative approaches in practice.
A Large Deformation Diffeomorphic Approach to Registration of CLARITY Images via Mutual Information
Venue: arXiv cs.CV 2017
Year: 2017

CLARITY is a method for converting biological tissues into translucent and porous hydrogel-tissue hybrids. This facilitates interrogation with light sheet microscopy and penetration of molecular probes while avoiding physical slicing. In this work, we develop a pipeline for registering CLARIfied mouse brains to an annotated brain atlas. Due to the novelty of this microscopy technique it is impractical to use absolute intensity values to align these images to existing standard atlases. Thus we adopt a large deformation diffeomorphic approach for registering images via mutual information matching. Furthermore we show how a cascaded multi-resolution approach can improve registration quality while reducing algorithm run time. As acquired image volumes were over a terabyte in size, they were far too large for work on personal computers. Therefore the NeuroData computational infrastructure was deployed for multi-resolution storage and visualization of these images and aligned annotations on the web.
Unsupervised Human Action Detection by Action Matching
Venue: arXiv cs.CV 2017
Year: 2017

We propose a new task of unsupervised action detection by action matching. Given two long videos, the objective is to temporally detect all pairs of matching video segments. A pair of video segments are matched if they share the same human action. The task is category independent---it does not matter what action is being performed---and no supervision is used to discover such video segments. Unsupervised action detection by action matching allows us to align videos in a meaningful manner. As such, it can be used to discover new action categories or as an action proposal technique within, say, an action detection pipeline. Moreover, it is a useful pre-processing step for generating video highlights, e.g., from sports videos. We present an effective and efficient method for unsupervised action detection. We use an unsupervised temporal encoding method and exploit the temporal consistency in human actions to obtain candidate action segments. We evaluate our method on this challenging task using three activity recognition benchmarks, namely, the MPII Cooking activities dataset, the THUMOS15 action detection benchmark and a new dataset called the IKEA dataset. On the MPII Cooking dataset we detect action segments with a precision of 21.6% and recall of 11.7% over 946 long video pairs and over 5000 ground truth action segments. Similarly, on THUMOS dataset we obtain 18.4% precision and 25.1% recall over 5094 ground truth action segment pairs.
Predicting Changes in Affective States using Neural Networks
Venue: arXiv cs.CY 2017
Year: 2017

Knowledge of patients affective state could prove to be crucial for health-care professionals in both diagnosis and treatment, however, this requires patients to report how they feel. In practice the sampling rate of affective states needs to be kept low, in order to ensure that the patients can rest. Furthermore using traditional methods of measuring affective states, is not always possible, e.g. patients can be incapable of verbal communications. In this study we explore the prediction of peoples self-reported affective state by measuring multiple physiological signals. We use different Neural networks (NN) setups and compare with different multiple linear regression (MLR) setups for prediction of changes in affective states. The results showed that NN and MLR predicted the change in affective states with accuracies of 91.88% and 89.10%, respectively.
Motif Clustering and Overlapping Clustering for Social Network Analysis
Venue: arXiv cs.SI 2017
Year: 2017

Motivated by applications in social network community analysis, we introduce a new clustering paradigm termed motif clustering. Unlike classical clustering, motif clustering aims to minimize the number of clustering errors associated with both edges and certain higher order graph structures (motifs) that represent "atomic units" of social organizations. Our contributions are two-fold: We first introduce motif correlation clustering, in which the goal is to agnostically partition the vertices of a weighted complete graph so that certain predetermined "important" social subgraphs mostly lie within the same cluster, while "less relevant" social subgraphs are allowed to lie across clusters. We then proceed to introduce the notion of motif covers, in which the goal is to cover the vertices of motifs via the smallest number of (near) cliques in the graph. Motif cover algorithms provide a natural solution for overlapping clustering and they also play an important role in latent feature inference of networks. For both motif correlation clustering and its extension introduced via the covering problem, we provide hardness results, algorithmic solutions and community detection results for two well-studied social networks.
Multi-Label Image Classification with Regional Latent Semantic Dependencies
Venue: arXiv cs.CV 2017
Year: 2017

Deep convolution neural networks (CNN) have demonstrated advanced performance on single-label image classification, and various progress also have been made to apply CNN methods on multi-label image classification, which requires to annotate objects, attributes, scene categories etc. in a single shot. Recent state-of-the-art approaches to multi-label image classification exploit the label dependencies in an image, at global level, largely improving the labeling capacity. However, predicting small objects and visual concepts is still challenging due to the limited discrimination of the global visual features. In this paper, we propose a Regional Latent Semantic Dependencies model (RLSD) to address this problem. The utilized model includes a fully convolutional localization architecture to localize the regions that may contain multiple highly-dependent labels. The localized regions are further sent to the recurrent neural networks (RNN) to characterize the latent semantic dependencies at the regional level. Experimental results on several benchmark datasets show that our proposed model achieves the best performance compared to the state-of-the-art models, especially for predicting small objects occurred in the images. In addition, we set up an upper bound model (RLSD+ft-RPN) using bounding box coordinates during training, the experimental results also show that our RLSD can approach the upper bound without using the bounding-box annotations, which is more realistic in the real world.
Novel Delivery Schemes for Decentralized Coded Caching in the Finite File Size Regime
Venue: arXiv cs.IT 2017
Year: 2017

This paper analyzes the achievable tradeoff between cache~size and download~rate in decentralized caching systems with the uncoded cache placement originally proposed by Maddah-Ali and Niesen. It proposes two novel delivery schemes that take advantage of the multicasting opportunities that arise when a file is demanded by multiple users. These delivery schemes are extensions of known ones to the regime where the file size is finite. Numerical evaluations for the case of file uniform popularity show that the proposed schemes outperform previous ones for all value of the cache size.
BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations
Venue: arXiv cs.NE 2017
Year: 2017

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling the Inferior- Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal- network dimensions but also different network-connectivity circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.